X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details PEG 3350, KMES, glycine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.99 α = 90
b = 66.27 β = 92.93
c = 75.89 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2010-05-03
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.100 NSLS X25

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.15 50 98.8 0.067 -- -- 3.7 20375 20375 3.0 3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.149 2.19 98.0 0.124 -- -- 3.7 1018

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.149 37.9 -- 0.0 20375 20375 1047 98.73 0.1789 0.1789 0.1755 0.2441 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.149 2.205 -- 78 1425 0.186 0.246 -- 98.04
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.2418
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.065
r_scbond_it 1.408
r_mcangle_it 1.019
r_mcbond_it 0.599
r_symmetry_hbond_refined 0.14
r_bond_refined_d 0.01
r_angle_refined_deg 1.324
r_dihedral_angle_1_deg 6.081
r_dihedral_angle_2_deg 38.757
r_dihedral_angle_3_deg 13.987
r_dihedral_angle_4_deg 13.307
r_chiral_restr 0.081
r_gen_planes_refined 0.004
r_nbd_refined 0.192
r_nbtor_refined 0.302
r_xyhbond_nbd_refined 0.127
r_symmetry_vdw_refined 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3128
Nucleic Acid Atoms 0
Heterogen Atoms 170
Solvent Atoms 196

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement
Phaser molecular replacement
SCALEPACK data scaling